Question: Novel MicroRNA prediction with Mirdeep 2.
gravatar for gurjeetkaur268
3.3 years ago by
gurjeetkaur26830 wrote:

I recently done small RNA sequencing of my endocrine tumour samples. I got result analysis with Mirdeep2 . I am not master in bioinformatics so , i outsourced the analysis. The company have predicted some novel micrornas. They have used mirdeep2 software for predicting novel microRNA.

I am facing problem in selecting novel microRNAs from small RNA sequencing. Is it necessary to have high mirdeep2 score with high mature read count. Those sequence with high mirdeep2 score ( like 3168) & mature read count (456) have non significant RANDFOLD p value. I am confused in this part.

I read in mirdeep2 documentation in which the score cut was from -10 to 10.but i am getting mirdeep2 score of like 3168 - 0. I am really very confused. Then i started comparing total read length , loop read length. But still confused.

Please guide me regarding mirdeep2 software and please help me its parameters for selecting novel microRNA.I thanks.

R • 1.7k views
ADD COMMENTlink written 3.3 years ago by gurjeetkaur26830

Hi, gurjeetkaur268, Can you solve the problem?. I also want to do sRNA analysis for Novel microRNA. Can you refer the company, please. Thank you in advance for your kind help.

ADD REPLYlink written 3.0 years ago by mahfuz.29006610

From the pdfs produced by miRDeep2, you can found that the miRDeep2 score were broken into several parts, including score for star reads, score for read counts, score for mfe, score for randfold, and score for cons. seed. Among of them, score for read counts always are the maximum. So, I speculate that the -10 to 10 splitting was for the sum of the scores excluding "score for read counts". This is just a guess.

ADD REPLYlink written 2.8 years ago by pengchy430
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